BioTEA: Containerized Methods of Analysis for Microarray-Based Transcriptomics Data

Abstract

Tens of thousands of gene expression data sets describing a variety of model organisms in many different pathophysiological conditions are currently stored in publicly available databases such as the Gene Expression Omnibus (GEO) and ArrayExpress (AE). As microarray technology is giving way to RNA-seq, it becomes strategic to develop high-level tools of analysis to preserve access to this huge amount of information through the most sophisticated methods of data preparation and processing developed over the years, while ensuring, at the same time, the reproducibility of the results. To meet this need, here we present bioTEA (biological Transcript Expression Analyzer), a novel software tool that combines ease of use with the versatility and power of an R/Bioconductor-based differential expression analysis, starting from raw data retrieval and preparation to gene annotation. BioTEA is an R-coded pipeline, wrapped in a Python-based command line interface and containerized with Docker technology. The user can choose among multiple options—including gene filtering, batch effect handling, sample pairing, statistical test type—to adapt the algorithm flow to the structure of the particular data set. All these options are saved in a single text file, which can be easily shared between different laboratories to deterministically reproduce the results. In addition, a detailed log file provides accurate information about each step of the analysis. Overall, these features make bioTEA an invaluable tool for both bioinformaticians and wet-lab biologists interested in transcriptomics. BioTEA is free and open-source.

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“…The workflow implemented in BioTEA v1.1.0 [ 111 ] was executed to acquire, preprocess, and conduct a DEA using microarray data from the selected datasets. Initially, the pipeline encompassed data retrieval from raw CEL files and data preprocessing stages.…”

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“…It enables intersections and unions among gene lists, with results displayed interactively via heatmaps, bar charts, Manhattan plots, and networks. BioTEA [ 11 ] is a Linux command line tool that performs microarray-based DGEAs. BioTEA facilitates data retrieval from microarray studies as well as the automatic parsing of their metadata, followed by differential analysis steps using simple commands up to the production of DEG lists, which could then be used for subsequent analysis.…”